Publication

Backmapping triangulated surfaces to coarse-grained membrane models

Pezeshkian, W., König, M., Wassenaar, T. A. & Marrink, S. J., 8-May-2020, In : Nature Communications. 11, 1, 9 p., 2296.

Research output: Contribution to journalArticleAcademicpeer-review

Many biological processes involve large-scale changes in membrane shape. Computer simulations of these processes are challenging since they occur across a wide range of spatiotemporal scales that cannot be investigated in full by any single current simulation technique. A potential solution is to combine different levels of resolution through a multiscale scheme. Here, we present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface (DTS) to its corresponding molecular model based on the coarse-grained (CG) Martini force field. Thus, we can use DTS simulations to equilibrate slow large-scale membrane conformational changes and then explore the local properties at CG resolution. We demonstrate the power of our method by backmapping a vesicular bud induced by binding of Shiga toxin and by transforming the membranes of an entire mitochondrion to near-atomic resolution. Our approach opens the way to whole cell simulations at molecular detail. Computer simulations of large-scale changes in membrane shape are challenging since they occur across a wide range of spatiotemporal scales. Here, authors present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface to its corresponding molecular model based on the coarse-grained Martini force field.

Original languageEnglish
Article number2296
Number of pages9
JournalNature Communications
Volume11
Issue number1
Publication statusPublished - 8-May-2020

    Keywords

  • SPONTANEOUS-CURVATURE, MOLECULAR-DYNAMICS, FORCE-FIELD, MECHANISM, PROTEINS, GROMACS, MARTINI, TOOL

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